Pocket Full of Broken Dreams: An Empire Undone
by madameHunterr
Summary: A new era has begun. Jessie-Lynn Adams fights against Alex Mercer, but helps him find the truth behind closed doors. Alex/OC. Rated: MA. [WARNING! Contains: Violence, Language, Sexuality/Nudity, and Lemons.]
1. Day Zero

**Author's Note: So here it is, the third sequence to my Prototype fanfic. :D I know a good amount of people have been looking forward to this, and I hope you all enjoy reading it, almost as much as I enjoy writing it ^_^  
><strong>

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><p><em>"My name is Alex Mercer. I'm the reason for all of this. They call me a killer, a monster, a terrorist...I'm all of these things."<em>  
>— Alex Mercer, opening line of the Prototype game.<p>

"His name is 'Mercer, Alex J.', next of kin, 'Mercer, Alaynah F.'; is that his wife?"

"Don't know."

"Do you think this has anything to do with the test subject on fifty-one?"

"I have no idea, and even more, I don't want to know. Just hand me the eight-inch blade. We'll start by going through the torso."

He woke up, about to be cut open by the attending pathologists. As they scrambled frantically, he rolled off the cadaver, hanging on for support. Looking around the room, he stood up and wobbled out the door to follow the men who'd already ran out the room.

He found his way out of the building and ran, stumbling from weakness and dizziness. He forced himself to continue and stopped by a truck, moving around it to peek from behind.

He observed as men came from the helicopter that came down and saw the pathologists speaking with them. Suddenly, the men in uniform shot the pathologists dead.

Alex swore, grabbing their attention and he ran to get away, but got himself cornered. He put his hands up as if to surrender, telling them to wait, but they all opened fire on him. The bullets riddled his body and he fell to his knees, getting up again and asking himself what was happening to him through the pain. He saw a gate behind a dumpster and ran for it, jumped onto the dumpster and jumped again, clearing the gate easily.

_I have to get the fuck out of here…_

He continued to run down the alley and over the other gate at the end, running through the streets and up buildings, a helicopter following him the whole time.

So there he was, running through the streets of New York like a madman, trying to understand what was going on while the army was after him too. He needed to lose them. And fast.

Still running down the street, the helicopter shot fire and he tripped, regaining control of himself, but holding up a taxi that was blown off of the ground and toward him in the process.

_What the fuck is going on?!_

He asked them what they were going to throw at him next; and asked what they wanted from him in the first place.

As men were being dispatched from the helicopter, Alex threw the taxi at the helicopter, blowing it up and killing the men that didn't even hit the ground yet. The helicopter fell straight down from the air and onto the street and Alex took his chance to run.

_I can't believe what I just did…_

He ran up a couple buildings and again up a taller one to get to a higher ground, and as he got to the top, two helicopters landed their sights on him.

Now I gotta kill them too…  
>He ripped off a structure attached to the ground and threw it at the helicopter. It spiralled as it went down and he proceeded to do the same thing to the other.<p>

_This can't be happening…_

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><p>Tired and dizzy, he found himself slumped down against the wall in an alley, and closed his eyes.<p>

A soldier had come up to him and he stayed still as he listened to what the soldier was saying, then the man shot him square in the forehead. The soldier advised that the 'target' was 'down', but didn't expect Alex to get up, grab him and flip him over, bashing his head into the ground. Tentacle-like membranes came out of Alex and surrounded the corpse of the soldier he just killed. A surge of pain went through him and he held his head, and suddenly something odd happened, he saw inside the mind of the soldier, his memories.

Suddenly hearing the sound of footsteps, he turned around and waited. He felt a tingle and looked at his body to realize that he had transformed into the soldier he had just killed. He stood there, waiting in his new disguise as the other soldier, who seemed to be of a higher rank than the soldier he was posing as. He stood still and waited as the soldier moved closer to him before grabbing him and tossing him on the ground, beating his face in and watched painfully as the tentacle structures did the same as it had done before. This time, however, he gathered some useful information.

He had a sister, named Dana; and he knew her apartment. He knew that these soldiers would be there, but he had to see her. She was probably the only one who could help him at that moment. So that's where he went, to her apartment.

Getting passed the soldiers was easy enough and upon entering, a soldier was holding Dana by her neck, between his forearm and torso.

"Dana?!" Alex exclaimed, pulling the man off his sister and punched through his entire body. The man fell dead and he proceeded to go to Dana. She seemed terrified, "I'm not going to hurt you." he reassured her. She kept backing up, eventually turning her head away.

He stood still and put his hand down, waiting for her to calm down; which she eventually did. They left the apartment and took temporary shelter under a bridge.

He asked for her help, but she was just as confused as he was. She explained that she was investigating to get him information, since he wanted to know what was going on in the higher levels of Gentek.

It caused him to have a flashback, of a person. Dr. Raymond McMullen, Director of Research. He didn't understand much of it.

They moved from under the bridge and took solace in a place which belonged to Dana's friends, who were away for the year.

Dana pointed out where Alex lived and he told her to stay put for her safety as he went to find his apartment.

Dana looked at the board after he left, _I wonder what Jess is going to say about all this…_

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><p><strong>I know it's short, but it's a start :P at least it's posted up now! :D<br>**

**Until next time, peace be upon you.**

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><p>≺) [ṃȧƌạṁeḤuɲʈǝrr]<p> 


	2. Day One

**Author's Note: Alright then, here's the next chapter. :D I'm not writing as much as I would like to with school going on and well...life haha..but I'm doing as much as I can.  
><strong>**Enjoy!**

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><p>He made his way over to his apartment. He was hoping to find at least something that would give him a hint of what was actually going on. But, upon entering, he saw clusters of useless information. A board with chalk written on it, a couple bookshelves with all sorts of different books—mainly scientific, computers…but what caught his attention the most were the pictures on the walls.<p>

There was a picture of Dana and some other woman with whom she was leaning on—though he didn't know who she was, there was a graduation certificate in his name, pictures of him and a child—a little girl, and a picture of him with another woman with blonde hair. His arm was wrapped around her.

He put his hand to the picture and in that instant, was sucked into some sort of painful flashback of the woman grabbing him by the arms—and then he came back to, looking around. He didn't understand what he saw, but he felt slightly more confused than before. He wasn't sure what that had to do with anything at all.

Suddenly, he was blasted out of the building, bombed. He went straight out the window. He recovered easily and landed on the ground. There was a tank there, and many men came out of his, now destroyed, apartment building, sheltering a man and bringing him into the vehicle.

_He's the one…_

As he was about to follow the tank, he was met by two helicopters, dispatching soldiers who were now shooting at him, hearing one state, "That thing is still alive!" He took out the soldiers easily, and evaded the 'Strike Team' that was now after him, going after the man who was being protected. He saw a helicopter pass by and heard through the radio that he obtained from the officer the night before, ordering men to an extraction point in Central Park. That's where he was headed next. The man who tried to kill him had to be there. He wasted no time in making his way over to the area. Whatever that man knew, he had to know.

Upon arriving at the extraction point, in Central Park, he got the message that the soldiers lost sight of him. He had to get the man out of the tank. Using the disguise of an officer, he sent out a message through the radio that the position was clear and safe for the man to exit the tank—and it worked. The man was now walking under the bridge in Central Park, almost completely open for Alex to make his move. He ran up to him and grabbed the man, tossed him to the ground and pummelled his face with his fists.

_Mercer's body is a bomb, filled with this weaponized pathogen, waiting to go off…_

He now knew what the man knew…

There was a clue of what was going on. He was infected with a virus that gave him the ability to do the things he could do, to change his arms into weapons, take on the disguise of others…it was all because of a virus. But how did he obtain the virus in the first place?

He evaded the soldiers and made his way back to Dana's hideout.

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><p>"What about your apartment?"<p>

"There's nothing left there." he said, leaving out the fact that he was blasted out of the window.

"Alright. I was thinking, the best person to talk to would be Jess. She should know what's going on."

"Jess?"

"Jessie."

"Who is Jessie?"

Dana stared at him blankly. Had he really forgotten? "_Jessie-Lynn Adams_." she reminded him. "Look, she lives here, alright? Just go and talk to her." she said, pointing to her location.

"Okay."

So that's where he headed, to this Jessie-Lynn Adams. She must have known something, why else would Dana suggest speaking with her?

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><p>Jessie was in between her balcony door and apartment, having a cigarette. She looked like a wreck. She still couldn't wrap her head around the fact that the one man she loved was now gone. Her face was stained with tears and her eyeliner didn't help at all.<p>

"Jessie-Lynn Adams?" Alex spoke.

Jessie turned around, startled at the sound of someone standing in her apartment. That's when she realized who it was.

"Alex?!"

"Yes?" he answered. He recognized her. She was the woman in the picture with Dana. She was the woman Dana was leaning on.

She ran up to him, wrapped her arms around his neck and kissed him. Alex felt the stinging pain of another flashback.

They were together. They were in love. They had…a child…? A daughter…and there she was, right there, playing with some toys on the living room floor.

"Baby, I thought you were dead. Oh, my God, I'm never letting you go again!" she cried, kissing him continuously.

He didn't react. He didn't know how to react to what she was doing.

"What's wrong?"

"Dana told me you know what's going on."

"Perhaps." she said, looking at the baby girl who was playing with her toys peacefully, until she saw Alex, and waddled over to him.

"What do you know?" Alex asked, ignoring the little human tugging on his pant leg.

"Why should I tell you?" she replied, her attitude changing almost immediately. He was taken back by the sudden change.

"I think you're the only one who could help me right now."

"I think you can and should find somebody else, because I'm not helping you."

"Why not?"

"As happy as I am to see you alive, I can't forgive you for what you did."

"What did I do?"

"Don't play stupid."

"I don't understand…"

"I said I'm not helping you, just go…" she said. He could see the battle she was having through her eyes before she turned around. She seemed unsure how to react to his presence.

And she didn't know. She didn't know whether to hold him and kiss him, not letting him out of her reach, or if she should slap him until his face was red for a few days.

When she turned around, he was gone.

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><p><strong>Hmm...that didn't seem to go the way he was expecting, lol.<br>Hopefully the next chapter will be up soon enough :D  
><strong>

**Keelah Se'lai, and Peace Be Upon You**

≺) [ṃȧƌạṁeḤuɲʈǝrr]


	3. Day Two

**Author's Note: Hello again! Sorry I haven't posted in a while. I actually can't remember the last post, haha. The same story as it usually is, school, school, more school. Anyway, I hope you enjoy this next chapter!**

**And Happy New Year!  
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><p><em><strong>Blackwatch Headquarters — RED CROWN Command, Battery Park…<strong>_

"_AXIOM_ will sweep to the river. _BRIMSTONE_ will encircle the entire sector and detain anyone movie through the area. I want this contained by daybreak."

"But, Sir, there are nearly a hundred thousand people in the blue zone."

"I'm _not_ interested in excuses. _Get it done_!"

The general turned off the screen and turned to the man who walked into the room just moments before his other conversation ended.

"We have a situation I think your team is well suited for, Captain. How long until your men are in place?" he asked.

"We're prepped and waiting for orders. We can be wheels up and boots on the ground anywhere in the city in fifteen." he replied, "With respect, Sir, a suppression operation in a city of twelve-million is slightly more than my men can handle."

"Of course it is, that's way beyond your league." Jessie, who was in the room the whole time, replied.

"Adams!" the general silenced her, turning back to the Captain, "That's not the situation I'm speaking of, you're not participating in that containment action. I'm pertaining to 'ZEUS'." he said, dropping files on the desk in front of him, "This conflict has evolved: he's carrying a new strain, has eliminated fifty of my men and smashed through a two-foot steel door. It's more than we thought it would be, but nothing you and your team can't handle."

_And he thinks dummy here can take Alex down?_ she thought to herself, holding back a chuckle.

"I'm your man, sir."

Jessie refrained from commenting about him taking any opportunity he can get to lick the General's boot.

"I don't need to tell you what's at stake."

"Sir."

"Dismissed."

With that, he gave a nod before leaving the room.

The general turned his attention to Jessie, "Captain Adams, you failed to eliminate Mercer when you were ordered to. However, the Blackwatch Organization is giving you a chance to make yourself…renewed. Find 'ZEUS' and take him down, no matter the cost, no matter what it takes."

"With all due respect, Sir, I'm the captain of the Stealth Team. Given my team's specialty, would this mission not be more appropriate for the Wisemen alone? You _did_ state that you believe his team can handle it."

"The Wisemen _will_ be working to obtain 'ZEUS'. The Stealth Team will be working alongside them."

"Sir?"

"The Wisemen are front and center, the Stealth Team will be in the shadows. We're pulling all stops to take down 'ZEUS'. His elimination is vital to the well being of this island. We can't have him running loose like a maniac."

"Yes, sir."

"Dismissed."

Jessie gave a nod before leaving.

_Fucker…_

"Jess." she heard a familiar voice and turned to see her husband.

"Cross?"

"I look forward to working with you."

"Go fuck yourself, kiss-ass."

"I know this may be hard for you, but this is your job and you're obligated to do what you're told. That was the deal with all of us when we joined the organization."

"You must be so happy that you finally get to fuck him up, aren't you?"

"I don't know what my feelings are toward this."

"That makes both of us." she said as she turned around and left to go to her office. Cross followed.

"Of course, there _is_ a part of me that is pleased to know he's getting what he deserves."

"And that would be what? Containing him and torturing him? Testing him like an animal? What _do_ you plan to do with him once you get him, Cross?"

"I'm not in the position to say what will happen; and I don't even know myself."

"_Right_."

Upon entering the office, Jessie turned to look at him.

"I'm just doing what _I_ have to in order to fix the problem that _your_ boyfriend created."

"You _cornered_ him at Penn Station!"

"So you're sticking up for him now?!"

"I didn't say that! I read the file, Cross. I know what you fuckers did to him."

"It had to be done." he said sternly.

"There was _no_ need to shoot him to death _after_ he did what you were _avoiding_. You people are fucking idiots. _Your_ men worsened the situation!"

"_My_ men are great at their job! At least they can carry out a task _before_ it's too late and needs someone else to clean up their mess!"

"Oh, you insufferable prick!"

"It wasn't that hard to do!"

"I was asked to execute the _father_ _of my child_!"

"He cheated on you!"

"That doesn't justify killing him so you morons could cover up your mistakes!"

"Stick up for the bastard all you want, it doesn't change the fact that we're cleaning up your mess."

"Get the fuck out of my sight!" she snarled and he did as told, slamming the door behind him.

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><p>"Are you sure you're up for this, Jess?" Kane asked her. Tension filled the air as they stared at each other for several moments before she finally looked away, breathing out a deep, anxious breath and closed her eyes, trying not to cry.<p>

"I have no choice." she said in an almost whisper, her voice slightly trembling.

"But you _do_ have a choice. You could leave."

"And throw away _everything_ that I've accomplished? I don't mean to sound too proud, but the truth of the matter is, Alex brought this upon himself. He needs to pay the consequences of his actions."

"Alright. Well, we're right behind you." he reassured her. She looked around the room, seeing not just her coworkers, but her friends. The people she'd gone into battle with, the people she'd shared laughs with for many years…all of them, nodding and reassuring her.

"Thank you." she said, trying not to cry once again from the support. Instead, it made her stronger and in that moment, she knew that whatever it was she had to do, she won't be alone.

_This is so crazy…_

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><p>After going over the information given to her about Alex, Jessie left work to pick up Alaynah from the daycare, heading to her apartment.<p>

Upon entering, she saw Alex standing there, looking at the photographs of the little girl and many other people that he didn't know. Still, many with him and Alaynah.

"What are you doing here?" she asked him as she put her daughter down, who trotted to Alex, hugging his leg. He looked down at her, unsure of what to do.

Jessie stared at him weirdly as he watched the little girl before hesitantly picking her up, upon which the little girl rested her head on his shoulder. He stood frozen.

"Alex."

"Yes?" he said, looking up from the little girl.

"_Why_ are you in my apartment?" she asked him again, an eyebrow quirking.

"I really need your help."

She sighed, pinching the bridge of her nose, "The answer is still no, Alex."

"_Please_," he begged, "I don't know who else to turn to. Dana said you could help, and I'm counting on that at this moment."

"Where is Dana?"

"Why?"

"I can't leave Alaynah here alone, Alex."

"Let me take her, then."

After a moment of thought, Jessie agreed, "Give me the coordinates."

"The what?" he asked, not hearing what she said the first time, since he was concentrating on the little girl at that moment.

"The _location_, Alex. Give me the location."

"You don't need to know."

"I think I have the right to know where our daughter is at _all_ times." she pointed out, getting a little irritated by his lack of cooperation.

Alex was still wrapping his head around the fact that this little girl was his own, and that the beautiful woman standing before him was the mother of his child. He wondered exactly how he lived his life before this whole fiasco happened…

"Alright, I'll tell you."

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><p>It was difficult running around with the little girl in his arms. He couldn't flip over stuff, only hold on to her and just run. She seemed very entertained and giggled a lot, and it made him slightly uncomfortable, but he understood that she was only a little girl and it was pleasing her. Nonetheless, he got her to Dana safely.<p>

"Dana." Alex said as he entered the hideout.

"So, I pulled up more informa—Alex?! What are you doing with Alaynah?!"

"Jessie knows I have her."

"Oh. Okay. For a second, I was about to say…"

"Jessie agreed to help me. She asked you to watch Alaynah."

"I can do that."

"She'll come back for her after."

"No problem. You should get going. You know how she is." Dana said as she took Alaynah from Alex.

"What?" Alex asked, confused a bit.

"Uh…nevermind, just go."

He nodded his head and left.

_He really can't remember anything…_

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><p>"So you're telling me that you can't remember <em>anything<em> at all?" Jessie asked, trying to understand the situation better.

He shook his head and raised his arms a bit, the way Alex Mercer usually would.

"This is going to be harder than I thought…"

"Why? Don't you know what happened?"

"I do."

"Then just tell me."

"It's easier said than done, Alex. Even if I wanted to, I can't bring the words out…on top of that, I don't know everything myself. We'll both be searching for answers."

"I see."

"I still can't believe this…"

"What?"

"_You_." she pointed her hand out toward him, "You're alive. You're…alive…you're standing in front of me, breathing, moving…"

"I shouldn't be."

"With how you died, no, you shouldn't be. I don't understand…"

"How did I die?"

"You…I…it.." she tried to explain, but couldn't.

The thought that Alex put the whole city in jeopardy to save his own ass seemed like something he would do, but the fact that he'd done it with his child in the city, she couldn't grasp that. There was something else. There had to have been. Alaynah meant everything to Alex, after his work, of course. Nothing came before that. She wanted answers herself. She wanted to know what was going on that night, what had caused him to do it…

Her pager went off and she looked at it.

"I'll see what I can do, Alex. I have to go."

"Okay."

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><p><strong>Well, looks like she wants to cooperate now. :) We'll see how it goes in the next chapter. <strong>

**Keelah Se'lai, and Peace Be Upon You.**

≺) [ṃȧƌạṁeḤuɲʈǝrr]


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